GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Utp12 - Dip2Utp12 Family
Pfam: PF04003 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Length: 110
Sequences: 620
Seq/Len: 5.64
HH_delta: 0.81 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
10_L52_L0.189352.076
101_G105_Y0.189052.072
67_L70_S0.151781.664
22_V58_A0.136851.500
70_S73_E0.136681.498
11_E48_H0.130271.428
38_S64_G0.129281.417
28_S37_L0.121881.336
87_E91_N0.121131.328
30_A34_L0.120251.318
50_E54_R0.119721.312
55_W64_G0.118581.300
67_L88_R0.118261.296
39_E61_K0.117811.291
7_L40_R0.116631.278
65_S69_S0.115591.267
5_L10_L0.114751.258
21_T85_L0.114381.254
41_L45_K0.113331.242
66_Y70_S0.113111.240
96_L102_R0.112651.235
10_L14_P0.110571.212
23_R51_F0.110031.206
21_T98_L0.109311.198
38_S84_I0.108711.192
87_E90_Q0.10681.171
38_S92_L0.105841.160
2_D13_I0.104181.142
17_D85_L0.104131.141
50_E99_N0.103891.139
98_L102_R0.102541.124
5_L55_W0.102321.122
6_L29_Y0.101941.117
22_V62_T0.101911.117
26_P29_Y0.101661.114
30_A63_H0.101031.107
51_F99_N0.099391.089
101_G109_Q0.098531.080
76_P105_Y0.097641.070
60_L95_L0.096921.062
22_V56_L0.095931.052
90_Q94_K0.095791.050
8_E106_L0.094871.040
104_D107_L0.094721.038
33_L109_Q0.094671.038
82_Q86_R0.094311.034
66_Y69_S0.094131.032
67_L72_P0.093961.030
18_I23_R0.092931.019
89_L93_S0.092841.018
23_R68_S0.09281.017
55_W60_L0.092181.010
28_S34_L0.092151.010
18_I91_N0.091661.005
21_T88_R0.091541.003
85_L93_S0.091341.001
48_H52_L0.090870.996
54_R58_A0.09080.995
4_E87_E0.090480.992
63_H66_Y0.089970.986
3_E9_V0.08950.981
18_I55_W0.089180.978
94_K99_N0.088810.973
51_F97_D0.088560.971
33_L46_S0.088150.966
31_E39_E0.087960.964
6_L98_L0.087730.962
8_E41_L0.08750.959
33_L45_K0.087490.959
14_P21_T0.087240.956
94_K107_L0.087190.956
10_L98_L0.087150.955
7_L24_S0.086720.951
52_L60_L0.086670.950
2_D17_D0.086360.947
30_A88_R0.086190.945
12_R45_K0.0860.943
24_S102_R0.085970.942
29_Y32_R0.085650.939
8_E78_L0.085480.937
9_V36_F0.085350.936
17_D50_E0.085320.935
83_K106_L0.085260.935
73_E81_L0.08470.928
78_L94_K0.084640.928
49_V81_L0.084550.927
2_D5_L0.083920.920
31_E67_L0.083630.917
25_L90_Q0.083370.914
74_L102_R0.083350.914
106_L109_Q0.083270.913
36_F65_S0.083010.910
13_I85_L0.082970.909
2_D21_T0.082880.908
72_P81_L0.082840.908
12_R87_E0.082390.903
22_V54_R0.081910.898
99_N102_R0.081890.898
60_L88_R0.081710.896
36_F105_Y0.081660.895
64_G87_E0.081440.893
50_E56_L0.080220.879
17_D104_D0.080150.879
2_D55_W0.080150.879
5_L24_S0.07930.869
8_E83_K0.079150.868
48_H101_G0.079070.867
9_V13_I0.079020.866
65_S108_S0.078960.865
39_E104_D0.078620.862
35_Q41_L0.078540.861
64_G85_L0.078490.860
5_L18_I0.078280.858
19_E58_A0.07810.856
25_L104_D0.0780.855
10_L105_Y0.077790.853
60_L83_K0.07760.851
22_V59_L0.077560.850
16_S25_L0.077470.849
32_R106_L0.077180.846
51_F76_P0.076990.844
36_F49_V0.076880.843
49_V99_N0.076650.840
41_L74_L0.076320.837
14_P36_F0.076230.836
23_R62_T0.076210.835
89_L92_L0.076140.835
98_L101_G0.075960.833
18_I60_L0.075760.830
52_L75_R0.075730.830
69_S87_E0.075710.830
46_S55_W0.075540.828
38_S56_L0.075510.828
26_P66_Y0.07530.825
52_L86_R0.075220.825
35_Q58_A0.075170.824
37_L70_S0.075150.824
47_P95_L0.074970.822
58_A61_K0.07480.820
7_L90_Q0.074770.820
21_T65_S0.074440.816
67_L95_L0.074430.816
76_P83_K0.074350.815
3_E39_E0.074220.814
21_T102_R0.074220.814
60_L103_L0.074110.812
36_F39_E0.07410.812
27_F66_Y0.074090.812
99_N105_Y0.074010.811
2_D98_L0.073820.809
19_E54_R0.073820.809
27_F54_R0.073770.809
19_E32_R0.073740.808
27_F56_L0.073390.804
31_E73_E0.073390.804
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
3s6n20.954589.30.81
3dwlG0.709189.10.81
1vu2F0.936487.20.816
1k8kG0.709184.10.824
2vxgA0.927349.80.861
4ffbC122.60.884
3w3wA0.345512.50.896
1ylmA0.46369.60.901
2rr7A0.69096.60.907
3pkrA0.82735.90.909
If you are interested in a protein containing this domain,
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